Compiling and running the PAMR wave example on vnfe4

NOTE: This build uses the Intel compilers, and the Myrinet OpenMPI/GM MPI library, which is the recommended practice at the current time (this is a change from pre-August 2008, when use of the PGI compilers and MPICH was recommended).

It is also assumed that you have DV running on your local workstation, and that, in your vnfe4 shell, you have set DVHOST to the name of said workstation.  Commands that you will need to type are in bold.

First ensure that the CVSROOT and CVS_RSH environment variables have been set 

setenv CVSROOT ':ext:cvs@vnfe4.physics.ubc.ca:/home2/cvs'
setenv CVS_RSH '/usr/bin/ssh'
(it is recommended that you insert the above in your ~/.cshrc).

Now cd to some convenient working directory and check out the pamr distribution 

% cvs co pamr
cvs server: Updating pamr
U pamr/.laliases
U pamr/KNOWN_ISSUES
       .
       .
       .
U pamr/test/Makefile.in
U pamr/test/test1.c
cvs server: Updating pamr/wave

Once the check-out is complete, change to the pamr directory, and build the distribution.  

% cd pamr
% source ~matt/scripts/soINTEL-myr-ompi
% configure --prefix=`pwd`
creating cache ./config.cache
checking for Unix flavour... LINUX
checking for gcc... 
       .
       .
       .
creating amrd/Makefile
creating examples/wave/Makefile
creating doc/Makefile
% make

for f in src amrd; do \
 (cd $f; make install) \
done
       .
       .
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cp: `../include/m_util_r8.h' and ... are the same file
cp: `../include/pamr.h' and ... are the same file
make[1]: [install] Error 1 (ignored)
make[1]: Leaving directory `/home3/vnfe4/home/...

Now change to the examples/wave directory and build the wave equation example.

% cd examples/wave
% make
Copy an appopriate PBS (Torque) batch submission file for the example, and submit the job---which uses 4 processors---to the batch queue using qsub
% cp ~matt/templates/pamr-wave-myr-openmpi.pbs .
% qsub pamr-wave-myr-openmpi.pbs
Wait for the batch job to finish: you can use the qstat command to monitor the status of the batch queue, but you can tell when the job has completed by the appearance of the standard output and standard error files associated with the job.  These will have names of the form pamr-wave.o[Job id] and pamr-wave.e[Job id] where [Job id] is the numeric part of the Job id which is returned by the qsub command.

Once the run has completed, change to the run_2d directory and you should see 4 .sdf  files, one for each of the 4 processors that were used in the sample computation.
% cd run_2d
% ls *sdf
wave_2d_L0_phi_tl2_0.sdf  wave_2d_L0_phi_tl2_2.sdf
wave_2d_L0_phi_tl2_1.sdf  wave_2d_L0_phi_tl2_3.sdf
% sdftodv *sdf
Then select Merge All Registers in DV, enable AMR in the Options panel, and visualize the results.
Maintained by choptuik@physics.ubc.ca. Supported by CIAR, CFI and NSERC